.TH FUNC 1 2006-09-02 "FUNC --RELEASE--"
.SH NAME
func-refin \- refines the results of the category test
.SH SYNOPSIS
.BR refin- YEAR-MM-DD .sh
.I [pvalue] [pvalue-after-refinement] [cutoff] 
.br
.SH DESCRIPTION
The refinement algorithm removes significant groups on a higher level if 
they are only significant because they include genes from significant subgroups. 
The result of the refinement are the most specific significant groups (as lower
groups give a more specific description of the data). 

The 
.BR refin- YEAR-MM-DD .sh
shellscript is created by one of the four 
.BR func (1)
tests. It 
will use the same output-directory, termdb-tables
and root-nodes as the invoked test.

.SH OPTIONS
.TP
.I [pvalue]
only the nodes, that are significant at this alpha are used for the refinement.
.TP
.I [pvalue-after-refinement]
after removal of the data of significant subgroups a significant group is
tested
with this alpha.
.TP
.I [cutoff]
only groups with at least 
.I cutoff
genes are tested. This cutoff is only applied before genes are removed.

.SH FILES
The refinement will place an resultfile for each root node 
into the output directory. The first columns describe the
Gene Ontology groups. The remaining 5 columns show

.IP 1.
+ if the group is significant after refinement, - otherwise
.IP 2.
left pvalue before refinement 
.IP 3.
right pvalue before refinement 
.IP 4.
left pvalue after refinement
.IP 5.
right pvalue after refinement

.LP 
A value of -1 after refinement means, that this node was'nt significant
before refinement. If the p value is -1 before the refinement, then the
node does'nt contain any data.

.LP
The resultfiles will be named 
refinement-\fBGO-ID\fR-\fIpvalue\fR-\fIpvalue-after-refinement\fR.txt.

.SH SEE ALSO
.BR func (1) 
.br
.B http://func.eva.mpg.de/
.br
.B --prefix--/doc/func---RELEASE--/ 
.br

.SH AUTHOR
Kay Pruefer <pruefer@eva.mpg.de>, Bjoern Muetzel <muetzel@eva.mpg.de>
